This work aimed to assess the potential of unmanned aerial vehicle (UAV) multi- and hyper-spectral platforms to estimate chlorophyll-a (Chl-a) and cyanobacteria in experimental fishponds in Brazil. In addition to spectral resolutions, the tested platforms differ in the price, payload, imaging system, and processing. Hyperspectral airborne surveys were conducted using a push-broom system 276-band Headwall Nano-Hyperspec camera onboard a DJI Matrice 600 UAV. Multispectral airborne surveys were conducted using a global shutter-frame 4-band Parrot Sequoia camera onboard a DJI Phantom 4 UAV. Water quality field measurements were acquired using a portable fluorometer and laboratory analysis. The concentration ranged from 14.3 to 290.7 µg/L and from 0 to 112.5 µg/L for Chl-a and cyanobacteria, respectively. Forty-one Chl-a and cyanobacteria bio-optical retrieval models were tested. The UAV hyperspectral image achieved robust Chl-a and cyanobacteria assessments, with RMSE values of 32.8 and 12.1 µg/L, respectively. Multispectral images achieved Chl-a and cyanobacteria retrieval with RMSE values of 47.6 and 35.1 µg/L, respectively, efficiently mapping the broad Chl-a concentration classes. Hyperspectral platforms are ideal for the robust monitoring of Chl-a and CyanoHABs; however, the integrated platform has a high cost. More accessible multispectral platforms may represent a trade-off between the mapping efficiency and the deployment costs, provided that the multispectral cameras offer narrow spectral bands in the 660–690 nm and 700–730 nm ranges for Chl-a and in the 600–625 nm and 700–730 nm spectral ranges for cyanobacteria.